Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays.

Modern improvement of complex traits in agricultural species relies on successful associations of heritable molecular variation with observable phenotypes. Historically, this pursuit has primarily been based on easily measurable genetic markers. The recent advent of new technologies allows assaying and quantifying biological intermediates (hereafter endophenotypes) which are now readily measurable at a large scale across diverse individuals. The usefulness of endophenotypes for delineating the regulatory landscape of the genome and genetic dissection of complex trait variation remains underexplored in plants. The work presented here illustrated the utility of a large-scale (299-genotype and seven-tissue) gene expression resource to dissect traits across multiple levels of biological organization. Using single-tissue- and multi-tissue-based transcriptome-wide association studies (TWAS), we revealed that about half of the functional variation acts through altered transcript abundance for maize kernel traits, including 30 grain carotenoid abundance traits, 20 grain tocochromanol abundance traits, and 22 field-measured agronomic traits. Comparing the efficacy of TWAS with genome-wide association studies (GWAS) and an ensemble approach that combines both GWAS and TWAS, we demonstrated that results of TWAS in combination with GWAS increase the power to detect known genes and aid in prioritizing likely causal genes. Using a variance partitioning approach in the largely independent maize Nested Association Mapping (NAM) population, we also showed that the most strongly associated genes identified by combining GWAS and TWAS explain more heritable variance for a majority of traits than the heritability captured by the random genes and the genes identified by GWAS or TWAS alone. This not only improves the ability to link genes to phenotypes, but also highlights the phenotypic consequences of regulatory variation in plants

Dosimeter-Type NOx Sensing Properties of KMnO4 and Its Electrical Conductivity during Temperature Programmed Desorption

An impedimetric NOx dosimeter based on the NOx sorption material KMnO4 is proposed. In addition to its application as a low level NOx dosimeter, KMnO4 shows potential as a precious metal free lean NOx trap material (LNT) for NOx storage catalysts (NSC) enabling electrical in-situ diagnostics. With this dosimeter, low levels of NO and NO2 exposure can be detected electrically as instantaneous values at 380 °C by progressive NOx accumulation in the KMnO4 based sensitive layer. The linear NOx sensing characteristics are recovered periodically by heating to 650 °C or switching to rich atmospheres. Further insight into the NOx sorption-dependent conductivity of the KMnO4-based material is obtained by the novel eTPD method that combines electrical characterization with classical temperature programmed desorption (TPD). The NOx loading amount increases proportionally to the NOx exposure time at sorption temperature. The cumulated NOx exposure, as well as the corresponding NOx loading state, can be detected linearly by electrical means in two modes: (1) time-continuously during the sorption interval including NOx concentration information from the signal derivative or (2) during the short-term thermal NOx release

Proceedings in Marine Biology

Journal of the Graduate Course of the Freie Universiät Berlin (Germany) at Kristinebergs Marina Forskningsstation (Sweden)Zeitschrift zur Kursreise der Freien Universität Berlin (Deutschland) an die Kristinebergs Marina Forskningsstation (Schweden)Peer Reviewe

A Test of Highly Optimized Tolerance Reveals Fragile Cell-Cycle Mechanisms Are Molecular Targets in Clinical Cancer Trials

Robustness, a long-recognized property of living systems, allows function in the face of uncertainty while fragility, i.e., extreme sensitivity, can potentially lead to catastrophic failure following seemingly innocuous perturbations. Carlson and Doyle hypothesized that highly-evolved networks, e.g., those involved in cell-cycle regulation, can be resistant to some perturbations while highly sensitive to others. The “robust yet fragile” duality of networks has been termed Highly Optimized Tolerance (HOT) and has been the basis of new lines of inquiry in computational and experimental biology. In this study, we tested the working hypothesis that cell-cycle control architectures obey the HOT paradigm. Three cell-cycle models were analyzed using monte-carlo sensitivity analysis. Overall state sensitivity coefficients, which quantify the robustness or fragility of a given mechanism, were calculated using a monte-carlo strategy with three different numerical techniques along with multiple parameter perturbation strategies to control for possible numerical and sampling artifacts. Approximately 65% of the mechanisms in the G1/S restriction point were responsible for 95% of the sensitivity, conversely, the G2-DNA damage checkpoint showed a much stronger dependence on a few mechanisms; ∼32% or 13 of 40 mechanisms accounted for 95% of the sensitivity. Our analysis predicted that CDC25 and cyclin E mechanisms were strongly implicated in G1/S malfunctions, while fragility in the G2/M checkpoint was predicted to be associated with the regulation of the cyclin B-CDK1 complex. Analysis of a third model containing both G1/S and G2/M checkpoint logic, predicted in addition to mechanisms already mentioned, that translation and programmed proteolysis were also key fragile subsystems. Comparison of the predicted fragile mechanisms with literature and current preclinical and clinical trials suggested a strong correlation between efficacy and fragility. Thus, when taken together, these results support the working hypothesis that cell-cycle control architectures are HOT networks and establish the mathematical estimation and subsequent therapeutic exploitation of fragile mechanisms as a novel strategy for anti-cancer lead generation

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Natural variability or anthropogenically-induced variation? Insights from 15 years of multidisciplinary observations at the arctic marine LTER site HAUSGARTEN

Time-series studies of arctic marine ecosystems are rare. This is not surprising since polar regions arelargely only accessible by means of expensive modern infrastructure and instrumentation. In 1999, theAlfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research (AWI) established the LTER(Long-Term Ecological Research) observatory HAUSGARTEN crossing the Fram Strait at about 79◦N.Multidisciplinary investigations covering all parts of the open-ocean ecosystem are carried out at a totalof 21 permanent sampling sites in water depths ranging between 250 and 5500 m. From the outset,repeated sampling in the water column and at the deep seafloor during regular expeditions in summermonths was complemented by continuous year-round sampling and sensing using autonomous instru-ments in anchored devices (i.e., moorings and free-falling systems). The central HAUSGARTEN stationat 2500 m water depth in the eastern Fram Strait serves as an experimental area for unique biologicalin situ experiments at the seafloor, simulating various scenarios in changing environmental settings.Long-term ecological research at the HAUSGARTEN observatory revealed a number of interesting tem-poral trends in numerous biological variables from the pelagic system to the deep seafloor. Contrary tocommon intuition, the entire ecosystem responded exceptionally fast to environmental changes in theupper water column. Major variations were associated with a Warm-Water-Anomaly evident in sur-face waters in eastern parts of the Fram Strait between 2005 and 2008. However, even after 15 years ofintense time-series work at HAUSGARTEN, we cannot yet predict with complete certainty whether thesetrends indicate lasting alterations due to anthropologically-induced global environmental changes of thesystem, or whether they reflect natural variability on multiyear time-scales, for example, in relation todecadal oscillatory atmospheric processes.peerReviewe